Harvard returned to the Caribbean with troops and supplies, arriving at Altares, Cuba, about 1 July. After Rear Admiral William T. Sampson's victory at the victory off Santiago, she rescued survivors. Despite the high surf and ammunition explosions from the stricken Spanish ships, Harvard succeeded in recovering over 600 officers and men. On 4 July 1898, the 9th Massachusetts Volunteer Infantry were guarding the prisoners of war inside Harvard. A guard ordered a prisoner, who was attempting to cross the line, to return. The prisoner did not understand English and the guard fired a shot causing other prisoners to stand up. Fearing the prisoners were about to attack, the guards opened fire, killing six prisoners and wounding thirteen more. After the investigation, it was concluded that it was a mistake. The tragedy was known as "Harvard Incident". No longer needed as a scout in the Caribbean, Harvard was sent back to the United States 10 July 1898. She was temporarily turned over to the War Department, and returned to Santiago de Cuba to transport troops back to the United States. Harvard arrived at New York on 27 August and decommissioned 2 September 1898 at New York Navy Yard. In 1901 she underwent a rebuild and was fitted with triple expansion engines, her funnels reduced from three to two, and her size increased to 10,798 tons. Post-war New York resumed her civilian service on the New York–Southampton run in January 1899. During her first post-war crossing, one of her engines broke down and she had to return to Southampton for repairs lasting three months. Three years later, New York was taken out of service for an extensive refit that included replacing her machinery with quadruple expansion engines. Her good looks were partly spoiled when her three raked funnels were replaced with two taller ones. She resumed service on 14 April 1903. On 10 April 1912, New York was berthed in Southampton beside . The three-inch steel hawsers that secured her were torn from their moorings when the much larger Titanic (leaving port to begin her ill-fated maiden voyage to New York City) passed by, creating a suction effect. A collision was narrowly avoided when Titanic's captain, Edward Smith, ordered the port propeller to reverse, turning the larger liner while the nearby tugboat Vulcan towed New York in the opposite direction. In 1913, New York was re-configured as a second and third-class